Decryption has a few dependencies that the latest client enforces. One should log out all other users, close all open applications and program especially e-mail applications. I can't say that I have heard of issues with multiple partitions previously.
Yes there is a standalone tool that can be used to decrypt files. The tool is designed to be run on systems where the client has been uninstalled. We may need to un-enroll the computer before running to tool. One caveat, at the moment the decryption tool is only available through the technical support.
Have you contacted technical support yet?